Pretty much all non-luxury housing in Tokyo is built to a much lower standard than equivalent housing built in say Canada or the US in the same time period.
Much thinner wall insulation, single glazed windows (until recently), much smaller elevators in high rises, etc…
So on a quality and square footage adjusted basis it’s still quite expensive.
Not really: the difference is that "lower standard" housing of the same age simply doesn't exist in the US. You want a small, 20-30 year old apartment in a decent building with small elevators and everything is maintained well and isn't broken, and you don't want roommates, and at an affordable price for you on your non-tech job paycheck? You can't have that in a decent American city; it doesn't exist. It's either some very expensive "luxury" apartment (where stuff is still broken, but hey, it has granite countertops and new appliances that'll break down in a year!) where you'll need roommates, or some nasty shithole (where you'll probably still need a rooomate).